[gmx-users] semiisotropic pressure coupling

[Mark Abraham]

Yongchul Chung wrote:
> Hello gmx-users,
> 
> I am running an NPT simulation with 100 molecules of n-alkane and trying 
> to impose uni-axial pressure of these molecules using semiisotropic 
> option in grompp.mdp.
> However, as the box seems to distort significantly due to the imposed 
> pressure which leads to the following error message:
> 
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.5
> Source code file: ns.c, line: 2295
> 
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length 
> or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> -------------------------------------------------------

You're imposing 1000 bar of pressure along the z-axis. Surely you should 
expect distortion?

You should do some maths and work out the expected density of the box 
under such pressure. You still need a box large enough that the maximum 
cut-off length can be satisfied, so that sets the minimum number of 
molecules you need, and thus the initial size of the box.

> I tried all vdwtype options to see whether this would mitigate the 
> issues but was unsuccessful.

Don't fool with .mdp settings hoping it'll magically work. Read how they 
work, and you might have understood why the minimum image convention 
requires that the condition that provoked the above error does not arise.

Mark

> is there any other options in gromacs that I can use to impose uniaxial 
> stress? Or does anyone had any similar problems related to 
> semi-isotropic pressure coupling?
> Thank you in advance.
> 
> This is my grompp.mdp file configuration:
> integrator          =  md
> dt                  =  0.001 ; ps !
> nsteps              =  1000000 ; 
> nstcomm             =  1
> nstxout             =  250 ; collect data every 0.5 ps
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> 
> coulombtype            =  PME
> rcoulomb            =  0.9
> vdwtype             =  switch
> rvdw                =  0.7
> rvdw_switch         =  0.0
> 
> fourierspacing  =  0.12
> fourier_nx  =  0
> fourier_ny  =  0
> fourier_nz  =  0
> pme_order  =  4
> ewald_rtol  =  1e-5
> optimize_fft  =  yes
> ; temperature coupling is on
> Tcoupl                      =  v-rescale
> ; Groups to couple separately
> tc-grps                  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t                    = 0.1
> ref_t                    = 300
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> constraints              = all-bonds
> 
> ; pressure coupling is on
> pcoupl = parrinello-rahman
> pcoupltype = semiisotropic
> 
> tau_p = 0.5
> compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction
> ref_p = 1.0 1000.0                  ;x/y-direction, z-direction
> 
> 
> 
> -- 
> Yongchul "Greg" Chung
> Graduate Student
> Dept. of Chemical Engineering, Case Western Reserve University
> 
> 
> ------------------------------------------------------------------------
> 
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